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- PDB-2qz2: Crystal structure of a glycoside hydrolase family 11 xylanase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qz2 | |||||||||
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Title | Crystal structure of a glycoside hydrolase family 11 xylanase from Aspergillus niger in complex with xylopentaose | |||||||||
![]() | Endo-1,4-beta-xylanase I | |||||||||
![]() | HYDROLASE / glycoside hydrolase / xylanase / Glycosidase / Xylan degradation | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Vandermarliere, E. / Rombouts, S. / Strelkov, S.V. / Delcour, J.A. / Courtin, C.M. / Rabijns, A. | |||||||||
![]() | ![]() Title: Crystallographic analysis shows substrate binding at the -3 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-beta-xylanases. Authors: Vandermarliere, E. / Bourgois, T.M. / Rombouts, S. / Van Campenhout, S. / Volckaert, G. / Strelkov, S.V. / Delcour, J.A. / Rabijns, A. / Courtin, C.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81 KB | Display | ![]() |
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PDB format | ![]() | 59.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2qz3C ![]() 2z79C ![]() 1ukrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19803.889 Da / Num. of mol.: 1 / Mutation: E170A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose |
#3: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS BELIEVE THAT THESE RESIDUES ARE CORRECT AND CONFIRM THAT THE ELECTRON DENSITY SHOWS ...THE AUTHORS BELIEVE THAT THESE RESIDUES ARE CORRECT AND CONFIRM THAT THE ELECTRON DENSITY SHOWS CLEAR EVIDENCE FOR THESE RESIDUES. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6M ammonium sulphate, 0.1M HEPES pH 7.5, 0.1 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 22, 2006 |
Radiation | Monochromator: Fixed exit double crystal Si [111], horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9918 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 6010 / Num. obs: 5843 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.4 / Rsym value: 0.094 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.8→2.85 Å / Mean I/σ(I) obs: 5.3 / Num. unique all: 271 / Rsym value: 0.302 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UKR Resolution: 2.8→19.48 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.852 / SU B: 32.331 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.812 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.802→2.874 Å / Total num. of bins used: 20
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